/*
 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
 * Copyright (C) $$Year-Rel$$ The Jalview Authors
 * 
 * This file is part of Jalview.
 * 
 * Jalview is free software: you can redistribute it and/or
 * modify it under the terms of the GNU General Public License 
 * as published by the Free Software Foundation, either version 3
 * of the License, or (at your option) any later version.
 *  
 * Jalview is distributed in the hope that it will be useful, but 
 * WITHOUT ANY WARRANTY; without even the implied warranty 
 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
 * PURPOSE.  See the GNU General Public License for more details.
 * 
 * You should have received a copy of the GNU General Public License
 * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
 * The Jalview Authors are detailed in the 'AUTHORS' file.
 */
package jalview.datamodel;

import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertFalse;
import static org.testng.AssertJUnit.assertNotNull;
import static org.testng.AssertJUnit.assertNull;
import static org.testng.AssertJUnit.assertSame;
import static org.testng.AssertJUnit.assertTrue;

import jalview.io.AppletFormatAdapter;
import jalview.io.FormatAdapter;
import jalview.util.MapList;

import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Iterator;
import java.util.List;

import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;

/**
 * Unit tests for Alignment datamodel.
 * 
 * @author gmcarstairs
 *
 */
public class AlignmentTest
{
  // @formatter:off
  private static final String TEST_DATA = 
          "# STOCKHOLM 1.0\n" +
          "#=GS D.melanogaster.1 AC AY119185.1/838-902\n" +
          "#=GS D.melanogaster.2 AC AC092237.1/57223-57161\n" +
          "#=GS D.melanogaster.3 AC AY060611.1/560-627\n" +
          "D.melanogaster.1          G.AGCC.CU...AUGAUCGA\n" +
          "#=GR D.melanogaster.1 SS  ................((((\n" +
          "D.melanogaster.2          C.AUUCAACU.UAUGAGGAU\n" +
          "#=GR D.melanogaster.2 SS  ................((((\n" +
          "D.melanogaster.3          G.UGGCGCU..UAUGACGCA\n" +
          "#=GR D.melanogaster.3 SS  (.(((...(....(((((((\n" +
          "//";

  private static final String AA_SEQS_1 = 
          ">Seq1Name/5-8\n" +
          "K-QY--L\n" +
          ">Seq2Name/12-15\n" +
          "-R-FP-W-\n";

  private static final String CDNA_SEQS_1 = 
          ">Seq1Name/100-111\n" +
          "AC-GG--CUC-CAA-CT\n" +
          ">Seq2Name/200-211\n" +
          "-CG-TTA--ACG---AAGT\n";

  private static final String CDNA_SEQS_2 = 
          ">Seq1Name/50-61\n" +
          "GCTCGUCGTACT\n" +
          ">Seq2Name/60-71\n" +
          "GGGTCAGGCAGT\n";
  // @formatter:on

  private AlignmentI al;

  /**
   * Helper method to load an alignment and ensure dataset sequences are set up.
   * 
   * @param data
   * @param format
   *          TODO
   * @return
   * @throws IOException
   */
  protected AlignmentI loadAlignment(final String data, String format)
          throws IOException
  {
    AlignmentI a = new FormatAdapter().readFile(data,
            AppletFormatAdapter.PASTE, format);
    a.setDataset(null);
    return a;
  }

  /*
   * Read in Stockholm format test data including secondary structure
   * annotations.
   */
  @BeforeMethod(alwaysRun = true)
  public void setUp() throws IOException
  {
    al = loadAlignment(TEST_DATA, "STH");
    int i = 0;
    for (AlignmentAnnotation ann : al.getAlignmentAnnotation())
    {
      ann.setCalcId("CalcIdFor" + al.getSequenceAt(i).getName());
      i++;
    }
  }

  /**
   * Test method that returns annotations that match on calcId.
   */
  @Test(groups = { "Functional" })
  public void testFindAnnotation_byCalcId()
  {
    Iterable<AlignmentAnnotation> anns = al
            .findAnnotation("CalcIdForD.melanogaster.2");
    Iterator<AlignmentAnnotation> iter = anns.iterator();
    assertTrue(iter.hasNext());
    AlignmentAnnotation ann = iter.next();
    assertEquals("D.melanogaster.2", ann.sequenceRef.getName());
    assertFalse(iter.hasNext());
  }

  @Test(groups = { "Functional" })
  public void testDeleteAllAnnotations_includingAutocalculated()
  {
    AlignmentAnnotation aa = new AlignmentAnnotation("Consensus",
            "Consensus", 0.5);
    aa.autoCalculated = true;
    al.addAnnotation(aa);
    AlignmentAnnotation[] anns = al.getAlignmentAnnotation();
    assertEquals("Wrong number of annotations before deleting", 4,
            anns.length);
    al.deleteAllAnnotations(true);
    assertEquals("Not all deleted", 0, al.getAlignmentAnnotation().length);
  }

  @Test(groups = { "Functional" })
  public void testDeleteAllAnnotations_excludingAutocalculated()
  {
    AlignmentAnnotation aa = new AlignmentAnnotation("Consensus",
            "Consensus", 0.5);
    aa.autoCalculated = true;
    al.addAnnotation(aa);
    AlignmentAnnotation[] anns = al.getAlignmentAnnotation();
    assertEquals("Wrong number of annotations before deleting", 4,
            anns.length);
    al.deleteAllAnnotations(false);
    assertEquals("Not just one annotation left", 1,
            al.getAlignmentAnnotation().length);
  }

  /**
   * Tests for realigning as per a supplied alignment: Dna as Dna.
   * 
   * Note: AlignedCodonFrame's state variables are named for protein-to-cDNA
   * mapping, but can be exploited for a general 'sequence-to-sequence' mapping
   * as here.
   * 
   * @throws IOException
   */
  @Test(groups = { "Functional" })
  public void testAlignAs_dnaAsDna() throws IOException
  {
    // aligned cDNA:
    AlignmentI al1 = loadAlignment(CDNA_SEQS_1, "FASTA");
    // unaligned cDNA:
    AlignmentI al2 = loadAlignment(CDNA_SEQS_2, "FASTA");

    /*
     * Make mappings between sequences. The 'aligned cDNA' is playing the role
     * of what would normally be protein here.
     */
    makeMappings(al1, al2);

    ((Alignment) al2).alignAs(al1, false, true);
    assertEquals("GC-TC--GUC-GTACT", al2.getSequenceAt(0)
            .getSequenceAsString());
    assertEquals("-GG-GTC--AGG--CAGT", al2.getSequenceAt(1)
            .getSequenceAsString());
  }

  /**
   * Aligning protein from cDNA.
   * 
   * @throws IOException
   */
  @Test(groups = { "Functional" })
  public void testAlignAs_proteinAsCdna() throws IOException
  {
    // see also AlignmentUtilsTests
    AlignmentI al1 = loadAlignment(CDNA_SEQS_1, "FASTA");
    AlignmentI al2 = loadAlignment(AA_SEQS_1, "FASTA");
    makeMappings(al1, al2);

    // Fudge - alignProteinAsCdna expects mappings to be on protein
    al2.getCodonFrames().addAll(al1.getCodonFrames());

    ((Alignment) al2).alignAs(al1, false, true);
    assertEquals("K-Q-Y-L-", al2.getSequenceAt(0).getSequenceAsString());
    assertEquals("-R-F-P-W", al2.getSequenceAt(1).getSequenceAsString());
  }

  /**
   * Test aligning cdna as per protein alignment.
   * 
   * @throws IOException
   */
  @Test(groups = { "Functional" }, enabled = false)
  // TODO review / update this test after redesign of alignAs method
  public void testAlignAs_cdnaAsProtein() throws IOException
  {
    /*
     * Load alignments and add mappings for cDNA to protein
     */
    AlignmentI al1 = loadAlignment(CDNA_SEQS_1, "FASTA");
    AlignmentI al2 = loadAlignment(AA_SEQS_1, "FASTA");
    makeMappings(al1, al2);

    /*
     * Realign DNA; currently keeping existing gaps in introns only
     */
    ((Alignment) al1).alignAs(al2, false, true);
    assertEquals("ACG---GCUCCA------ACT", al1.getSequenceAt(0)
            .getSequenceAsString());
    assertEquals("---CGT---TAACGA---AGT---", al1.getSequenceAt(1)
            .getSequenceAsString());
  }

  /**
   * Test aligning cdna as per protein - single sequences
   * 
   * @throws IOException
   */
  @Test(groups = { "Functional" }, enabled = false)
  // TODO review / update this test after redesign of alignAs method
  public void testAlignAs_cdnaAsProtein_singleSequence() throws IOException
  {
    /*
     * simple case insert one gap
     */
    verifyAlignAs(">dna\nCAAaaa\n", ">protein\nQ-K\n", "CAA---aaa");

    /*
     * simple case but with sequence offsets
     */
    verifyAlignAs(">dna/5-10\nCAAaaa\n", ">protein/20-21\nQ-K\n",
            "CAA---aaa");

    /*
     * insert gaps as per protein, drop gaps within codons
     */
    verifyAlignAs(">dna/10-18\nCA-Aa-aa--AGA\n", ">aa/6-8\n-Q-K--R\n",
            "---CAA---aaa------AGA");
  }

  /**
   * Helper method that makes mappings and then aligns the first alignment as
   * the second
   * 
   * @param fromSeqs
   * @param toSeqs
   * @param expected
   * @throws IOException
   */
  public void verifyAlignAs(String fromSeqs, String toSeqs, String expected)
          throws IOException
  {
    /*
     * Load alignments and add mappings from nucleotide to protein (or from
     * first to second if both the same type)
     */
    AlignmentI al1 = loadAlignment(fromSeqs, "FASTA");
    AlignmentI al2 = loadAlignment(toSeqs, "FASTA");
    makeMappings(al1, al2);

    /*
     * Realign DNA; currently keeping existing gaps in introns only
     */
    ((Alignment) al1).alignAs(al2, false, true);
    assertEquals(expected, al1.getSequenceAt(0).getSequenceAsString());
  }

  /**
   * Helper method to make mappings between sequences, and add the mappings to
   * the 'mapped from' alignment
   * 
   * @param alFrom
   * @param alTo
   */
  public void makeMappings(AlignmentI alFrom, AlignmentI alTo)
  {
    int ratio = (alFrom.isNucleotide() == alTo.isNucleotide() ? 1 : 3);

    AlignedCodonFrame acf = new AlignedCodonFrame();

    for (int i = 0; i < alFrom.getHeight(); i++)
    {
      SequenceI seqFrom = alFrom.getSequenceAt(i);
      SequenceI seqTo = alTo.getSequenceAt(i);
      MapList ml = new MapList(new int[] { seqFrom.getStart(),
          seqFrom.getEnd() },
              new int[] { seqTo.getStart(), seqTo.getEnd() }, ratio, 1);
      acf.addMap(seqFrom, seqTo, ml);
    }

    alFrom.addCodonFrame(acf);
  }

  /**
   * Test aligning dna as per protein alignment, for the case where there are
   * introns (i.e. some dna sites have no mapping from a peptide).
   * 
   * @throws IOException
   */
  @Test(groups = { "Functional" }, enabled = false)
  // TODO review / update this test after redesign of alignAs method
  public void testAlignAs_dnaAsProtein_withIntrons() throws IOException
  {
    /*
     * Load alignments and add mappings for cDNA to protein
     */
    String dna1 = "A-Aa-gG-GCC-cT-TT";
    String dna2 = "c--CCGgg-TT--T-AA-A";
    AlignmentI al1 = loadAlignment(">Dna1/6-17\n" + dna1
            + "\n>Dna2/20-31\n" + dna2 + "\n", "FASTA");
    AlignmentI al2 = loadAlignment(
            ">Pep1/7-9\n-P--YK\n>Pep2/11-13\nG-T--F\n", "FASTA");
    AlignedCodonFrame acf = new AlignedCodonFrame();
    // Seq1 has intron at dna positions 3,4,9 so splice is AAG GCC TTT
    // Seq2 has intron at dna positions 1,5,6 so splice is CCG TTT AAA
    MapList ml1 = new MapList(new int[] { 6, 7, 10, 13, 15, 17 }, new int[]
    { 7, 9 }, 3, 1);
    acf.addMap(al1.getSequenceAt(0), al2.getSequenceAt(0), ml1);
    MapList ml2 = new MapList(new int[] { 21, 23, 26, 31 }, new int[] { 11,
        13 }, 3, 1);
    acf.addMap(al1.getSequenceAt(1), al2.getSequenceAt(1), ml2);
    al2.addCodonFrame(acf);

    /*
     * Align ignoring gaps in dna introns and exons
     */
    ((Alignment) al1).alignAs(al2, false, false);
    assertEquals("---AAagG------GCCcTTT", al1.getSequenceAt(0)
            .getSequenceAsString());
    // note 1 gap in protein corresponds to 'gg-' in DNA (3 positions)
    assertEquals("cCCGgg-TTT------AAA", al1.getSequenceAt(1)
            .getSequenceAsString());

    /*
     * Reset and realign, preserving gaps in dna introns and exons
     */
    al1.getSequenceAt(0).setSequence(dna1);
    al1.getSequenceAt(1).setSequence(dna2);
    ((Alignment) al1).alignAs(al2, true, true);
    // String dna1 = "A-Aa-gG-GCC-cT-TT";
    // String dna2 = "c--CCGgg-TT--T-AA-A";
    // assumption: we include 'the greater of' protein/dna gap lengths, not both
    assertEquals("---A-Aa-gG------GCC-cT-TT", al1.getSequenceAt(0)
            .getSequenceAsString());
    assertEquals("c--CCGgg-TT--T------AA-A", al1.getSequenceAt(1)
            .getSequenceAsString());
  }

  @Test(groups = "Functional")
  public void testCopyConstructor() throws IOException
  {
    AlignmentI protein = loadAlignment(AA_SEQS_1, FormatAdapter.PASTE);
    // create sequence and alignment datasets
    protein.setDataset(null);
    AlignedCodonFrame acf = new AlignedCodonFrame();
    List<AlignedCodonFrame> acfList = Arrays.asList(new AlignedCodonFrame[]
    { acf });
    protein.getDataset().setCodonFrames(acfList);
    AlignmentI copy = new Alignment(protein);

    /*
     * copy has different aligned sequences but the same dataset sequences
     */
    assertFalse(copy.getSequenceAt(0) == protein.getSequenceAt(0));
    assertFalse(copy.getSequenceAt(1) == protein.getSequenceAt(1));
    assertSame(copy.getSequenceAt(0).getDatasetSequence(), protein
            .getSequenceAt(0).getDatasetSequence());
    assertSame(copy.getSequenceAt(1).getDatasetSequence(), protein
            .getSequenceAt(1).getDatasetSequence());

    // TODO should the copy constructor copy the dataset?
    // or make a new one referring to the same dataset sequences??
    assertNull(copy.getDataset());
    // assertArrayEquals(copy.getDataset().getSequencesArray(), protein
    // .getDataset().getSequencesArray());
  }

  /**
   * Test behaviour of createDataset
   * 
   * @throws IOException
   */
  @Test(groups = "Functional")
  public void testCreateDatasetAlignment() throws IOException
  {
    AlignmentI protein = new FormatAdapter().readFile(AA_SEQS_1,
            AppletFormatAdapter.PASTE, "FASTA");
    /*
     * create a dataset sequence on first sequence
     * leave the second without one
     */
    protein.getSequenceAt(0).createDatasetSequence();
    assertNotNull(protein.getSequenceAt(0).getDatasetSequence());
    assertNull(protein.getSequenceAt(1).getDatasetSequence());

    /*
     * add a mapping to the alignment
     */
    AlignedCodonFrame acf = new AlignedCodonFrame();
    protein.addCodonFrame(acf);
    assertNull(protein.getDataset());
    assertTrue(protein.getCodonFrames().contains(acf));

    /*
     * create the alignment dataset
     * note this creates sequence datasets where missing
     * as a side-effect (in this case, on seq2
     */
    // TODO promote this method to AlignmentI
    ((Alignment) protein).createDatasetAlignment();

    // TODO this method should return AlignmentI not Alignment !!
    Alignment ds = protein.getDataset();

    // side-effect: dataset created on second sequence
    assertNotNull(protein.getSequenceAt(1).getDatasetSequence());
    // dataset alignment has references to dataset sequences
    assertEquals(ds.getSequenceAt(0), protein.getSequenceAt(0)
            .getDatasetSequence());
    assertEquals(ds.getSequenceAt(1), protein.getSequenceAt(1)
            .getDatasetSequence());

    // codon frames should have been moved to the dataset
    // getCodonFrames() should delegate to the dataset:
    assertTrue(protein.getCodonFrames().contains(acf));
    // prove the codon frames are indeed on the dataset:
    assertTrue(ds.getCodonFrames().contains(acf));
  }

  @Test(groups = "Functional")
  public void testAddCodonFrame()
  {
    AlignmentI align = new Alignment(new SequenceI[] {});
    AlignedCodonFrame acf = new AlignedCodonFrame();
    align.addCodonFrame(acf);
    assertEquals(1, align.getCodonFrames().size());
    assertTrue(align.getCodonFrames().contains(acf));
    // can't add the same object twice:
    align.addCodonFrame(acf);
    assertEquals(1, align.getCodonFrames().size());

    // create dataset alignment - mappings move to dataset
    ((Alignment) align).createDatasetAlignment();
    assertSame(align.getCodonFrames(), align.getDataset().getCodonFrames());
    assertEquals(1, align.getCodonFrames().size());

    AlignedCodonFrame acf2 = new AlignedCodonFrame();
    align.addCodonFrame(acf2);
    assertTrue(align.getDataset().getCodonFrames().contains(acf));
  }

  @Test(groups = "Functional")
  public void getVisibleStartAndEndIndexTest()
  {
    Sequence seq = new Sequence("testSeq", "ABCDEFGHIJKLMNOPQRSTUVWXYZ");
    AlignmentI align = new Alignment(new SequenceI[] { seq });
    ArrayList<int[]> hiddenCols = new ArrayList<int[]>();

    int[] startEnd = align.getVisibleStartAndEndIndex(hiddenCols);
    assertEquals(0, startEnd[0]);
    assertEquals(25, startEnd[1]);

    hiddenCols.add(new int[] { 0, 0 });
    startEnd = align.getVisibleStartAndEndIndex(hiddenCols);
    assertEquals(1, startEnd[0]);
    assertEquals(25, startEnd[1]);

    hiddenCols.add(new int[] { 6, 9 });
    hiddenCols.add(new int[] { 11, 12 });
    startEnd = align.getVisibleStartAndEndIndex(hiddenCols);
    assertEquals(1, startEnd[0]);
    assertEquals(25, startEnd[1]);

    hiddenCols.add(new int[] { 24, 25 });
    startEnd = align.getVisibleStartAndEndIndex(hiddenCols);
    System.out.println(startEnd[0] + " : " + startEnd[1]);
    assertEquals(1, startEnd[0]);
    assertEquals(23, startEnd[1]);
  }
}